Biology Midterm 1 typed set Flashcards
(109 cards)
1
Q
Where are most of the genes held in eukaryotic cells?
A
The nucleus
2
Q
How is the nucleus composed in eukaryotic cells?
A
Double membrane nuclear envelope surrounds nucleus, enclosing genetic material (chromosomes) and separates nuclear contents from the cytoplasm
The nucleolus is where rRNA is transcribed. The rRNA binds to proteins to form ribosomal subunits. Then it is exported out to the cytoplasm.
The nuclear pore complexes allows materials to flow in and out of the cell.
The chromosomes are within the middle of the nucleus between the nuclear membrane and the nucleolus
3
Q
Where are the structure components of rRNA synthesized?
A
In the nucleolus, then the subunits of ribosomes containing protein and RNA form, and ship out to the cytoplasm
4
Q
What are the options of ribosomes after they have been shipped out?
A
They can remain soluble in the cytoplasm as free ribosomes
OR
Attach onto the ER and become bound ribosomes
5
Q
Bound ribosomes
A
Ribosomes on the ER
6
Q
Free ribosomes
A
Ribosomes that are freely within the cytoplasm
7
Q
Draw out and describe the structure of an amino acid
A
Refer to notes
8
Q
How many amino acids in total are there
A
20
9
Q
What is the only difference between the amino acid monomers which determines the properties of the entire amino acid
A
The R-group
10
Q
Amino acid polymers called
A
polypeptides
11
Q
How are amino acids formed
A
Through condensation reactions
12
Q
Bonds between amino acids called
A
peptide bonds
13
Q
Primary structure of proteins
A
The unique sequence of amino acids which form the polypeptide with varying R-groups
14
Q
What does tRNA do
A
Carries the correct amino acid to the next position of the growing chain
15
Q
What step of DNA replication is where amino acids are joined together?
A
Translation -> forms the primary structure
Transcription produces the mRNA which contains the code for translation into the actual amino acid chain
16
Q
How do bonds specifically form between amino acids?
A
Between the carboxyl and amino group a C-N peptide bond forms
17
Q
Alipathic amino acids
A
Hydrocarbon (akyl) chains and a benzene ring
18
Q
Explain the destination of proteins after translation has been complete (in terms of the ribosomes they’re synthesized by)
A
Bound ribosomes (ER)
-could remain in cytosol
-enzymes for glycolysis or structural proteins of cell
-targeted to various cell organelles
Proteins synthesized by free ribosomes
-found in cytosol
-can be transported into the nucleus
-histone proteins or transcription factors
-head to the mitochondria or chloroplasts
-become membrane proteins in these organelles
19
Q
How does a polypeptide obtain it’s shape?
A
By the interactions between the R-groups
20
Q
Secondary structure + the types of secondary structures
A
The interaction between the protein’s backbone
Alpha helix
-spiral/coil due to their hydrogen bonds
- Carbonyl of carboxyl group one 1 amino acid + amide of amino group of another amino acid 4 positions away
-R groups stick out of helix due to hydrogen bonds
Beta plated sheets
-parallel proteins strands with hydrogen bonds formed between carboxyl and amino groups
21
Q
Tertiary structure
A
The interactions between R-groups which allow the protein to bend and fold and obtain it’s 3D shape
bonds: H-bonds, london, ionic, disulfide, hydrophobic interactions, covalent
-forms properly folded proteins
-helps support and hold the shape
22
Q
What are the two assistants that help with protein folding, describe them
A
Molecular chaprones:
proteins that bind to the hydrophobic regions of the polypeptide and prevent incorrect folding
Chaperonins: molecular complexes which form isolation chambers with a protein inside so it can fold without interference
23
Q
Quartneary structure
A
The assmebling of different subunits of tertiary structures to form the fully functional protein
24
Q
Endomembrane system components
A
lysosome, ER, golgi, vacuoles, nuclear envelope
for protein and lipid synthesis
25
How were today's eukaryotes derived (endomembrane system)
From the invagination of an ancestral prokaryote which contained genetic, heritable material.
26
Explain what happens when a ribosome becomes bound to the ER (all steps 7 + substeps)
1. mRNAs that code for proteins for the endomembrane system have a special signal sequence that once translated, causes the ribosomes to become bound to the ER.
2. The protein then enters the lumen for further processing (folding)
3. It can then either leave or continue to the final destination by vesicles pinching off the ER
- if it stays then it can undergo **glycosylation** which is the addition of a carbohydrate chain in a protein
-cell to cell recognition, stability, folding
4. The vesicles will fuse with the golgi apparatus and deposit their contents into the golgi lumen
5. Further protein modification will occur
-glycosylation can also occur here
Proteins either stay or leave again through vesicles
6. proteins go to several different destinations
1. cell membrane (porins/receptors/transmembrane proteins)
2. secreted out of cell (antibodies, hormones, enzymes)
3. other organelles (lysosome, vacuoles)
They are all sorted by a TAG which allows it to be transported through a certain vesicle and can fuse their contents with the phospholipid bilayer of destination
7. These vesicles reach their proper location by the cytoskeleton which is a dense network of fibers that maintain/change cell shape
-microtubules stretch through the cell
-cellular roadways
-kinesin nd dynein attach transport vesicle and walk along microtubules using ATP
27
What is glycosylation
Then addition of a carbohydrate chain onto a protein
-usually occurs on membrane bound proteins
-protein stability, folding, and cell-to-cell recognition
28
How do vesicles reach their locations?
They are assisted by the cytoskeleton which maintains the structure of the cell by microtubules which vesicle attaches onto kinesin and dyenin and they walk along the microtubules.
29
What kind of DNA do prokaryotic cells have?
They have cirucular DNA called plasmids or in their nucleoid (majority in here)
Circular DNA
-carries 1 to 2 genes
-replicate independetly of core genome
-transferred from one cell to another
30
Why do bacteria replicate so fast?
They contain circular DNA which replicate independently of their core genome and are able to move from one cell to another
31
Chromosome composition
Contains DNA and proteins and RNAs
32
Difference between prokaryotic and eukaryotic chromsomes
Prokaryotic: nucleoid + circular chromosomes
-> these are supercoiled into loops
Eukaryotic: large linear chromosomes
33
Supercoiling
A way of compacting DNA while perserving the double helix structure
34
What would be the purpose of circular DNA in prokaryotes?
They could contain chromosomal DNA with genes needed for survival
35
How did Griffith/neufled disvoer the hereditary material
They discovered that a hereditary material that could cause a cell to change
Took S-strain
R-strain
heated killed S-strain + R strain = dead
Heated s strain = alive
He realized that the R-strain had undergone transformation meaning that it had uptaken some genetic hereditary material from outside of its cell.
36
Avery, McLead and Mccarty
They discovered that the DNA molecule was the hereditary material in the cell.
They took enzymes to kill a certain macromolecule leaving the rest alive and observed which one was the hereditary material
37
Subunits of DNA
nucleotides
38
What is the composition of a nucleotide
phosphate group
5-carbon deoxyribose sugar
nitrogenous base
39
Pyrimidines
Cytosine and thymine
40
Purines
Guanine and adenine
41
Explain the bonding of nucleotides !!!!!!!!!!!!!!
A phosphodiester bond forms between 2 nucleotides
The 5' carbon forms a bond with the 3' carbon on the next deoxyribose
Backbone is in 5' to 3' polarity !!!
- added to the 3' end
Nitrogenous base sticks out of the backbone
42
What end are nucleotides added
3' end
Goes in 5' to 3' direction
43
Rosalind Franklin discoveries(4)
She used X-ray cystallography to bombard samples of DNA and then it defracted a shape
-she discovered the helical nature
-discovered the sugar phosphate backbone faced out
-x-shape suggesting a clockwise model
-2 H bonds between AT and 3 between GC
44
How many hydrogen bonds between each nucleotide pairing?
AT - 2
GC - 3
45
Watson and Crick (4)
-they summarized the shape
-bases face inwards 2.0nm
-consists of two long chains of nucleotides running antiparellel
-turn of helix every 10 seconds
46
What makes RNA
RNA polymerase adds ribonucleotides to the mRNA growing chain through hydrogen bonding
47
What does uracil replace
Thymine
48
How are phosphodiester bonds formed in the RNA backbone?
The 3' hydroxyl attacks the high energy phosphate of the new ribonucleotide and the phosphodiester bond is formed
Hydrogen bonds are formed between the nucleotides
49
mRNA
the RNA copy of the genes coding for a protein
50
tRNA
Functional RNA
Never translated
Attach onto amino acids and brings them to the growing chain
51
rNA
ribosomal DNA
synthesized in the nucleolus
-subunits assmeble as well as proteins
-large proportion of total RNA
52
How are chromosomes formed?
DNA -> chromatin fiber surround histone proteins -> coiling creates a chromotain fiber
-> continue coiling
-> chromosome
53
What ribosomes become bound to the membrane of the rough ER
free ribosomes?
54
Explain the SRP receptor and the speical signal
Signal recognition particle SRP will attach onto a special recongition signal sequence in the growing polypeptide-chain and stops translation
The SRP binds onto the SRP receptor on the ER membrane
SRP reeleased and the ribosome will come to the transmembrane channel and release the growing polypeptide chain
The protein ends up in lumen
55
Cystic fibrosis
A genetic disease that has greatest impacts on digestion and the lungs
-cough, thick mucus, wheezing, chest infection, bowel disturbance, salty sweat
56
What do symptoms of cytstic fibrosis root from?
The innapropriate transport of ions and water across the cell membrane which cause the ducts to be compromised
57
Explain cystic fibrosis and the reason it occurs (use all nesscary terms)
Goblet cells are cells in the epithetial cells of airways which are responsible for producing mucus. The mucus is key in order to clear out dust and environment pollutants and bacteria. Ciliated projections on the epithelial cells serves as ways for mucus to be cleared. (continue to edit)
58
Genes
sections of DNA molecule which contain information that is transcribed into a copy of RNA
59
Central dogma
DNA -> transcription -> mRNA -> translation -> protein
Information stored in the DNA acts like a blueprint which will specify the RNA sequence and then specify the sequence of amino acids in a protein. mRNA molecules are then translated from nucleotide into amino acids of protein.
60
Template strand, RNA, nontemplate strand
Template strand: the strand of DNA serving as a template for RNA transcription
RNA: the mRNA which is paired with nucleotides to the template strand
The mRNA strand is antiparellel to the template DNA strand
Non-template strand: the non-template strand which has the same sequence as the RNA
61
Where does RNA polymerase attach to? How are they situated?
It attaches to promoter regions which are transcriptional starting points where RNA synthesis begins
They are situated upstream 5' relative to the gene of interest
62
5' end =
3' end =
5' end = 5' phosphate on a nucleotide
3' end = 3' OH group on a nucleotide
63
Explain the steps that happens after RNA polymerase binds (Initiation of transcription)
It binds onto a promoter and begins to move along the DNA and opens up the double-stranded DNA revealing the template and non-template strand within a transcription bubble.
It then begins to form a DNA RNA duplex is created
Template strand is "read" in 3'-5' direction and RNA is synthesized in 5'->3' direction
Once bound, template strand undergoes an "open conformation" and then transcription occurs along the length of a gene and RNA polyerase elongates one nucleotide at a time
structural features of RNA polymerase seperate the two strands forming the transcription bubble
64
Explain elongation of DNA replication in replication
Ribonucleotides are able to enter the RNA polymerase and assemble in a complementary fashion on the DNA template strand
Transcription continues, RNA polymerase passes the DNA through a channel, transcribe the template into an mRNA strand, and then threads the same DNA through another channel
RNA polymerase is able to restore the DNA double helix once transcript is produced along with splitting the DNA helixes
RNA polymerase moves downstream from the promoter region and unwinds the DNA helix and creates the **RNA polynucleotide transcript**
1 single gene is able to be transcribed by several RNA polymerase at the same time
This allow
The RNA polymerase continues to add ribonucleotides to the 3' end of the elongating RNA transcript.
65
How are cells able to make a lot of RNA copies at the same time? (englongation)
There are multiple RNA polymerase that are able to transcribe genes into RNA at the same time
66
Explain the process of RNA ribonucleotides being added to the 3' end. What process is being used to bind?
The incoming ribonucleotide triphosphates are going to be added to the 3' end of the elongating RNA transcript.
Each of these ribonucleotide triphosphate are going to correctly base pair with the template DNA
The 3'-OH of the growing chain is going to attack the high eneryg phosphate bond of the incoming ribonucleotide
The high potential energy of the phosphate bonds of the incoming ribonucleotide triphosphate is used to drive the high energy process which is required to make a **phosphodiester bond** between the incoming nucleotide and the growing RNA transcript
This release and cleveage of the pyrophosphate group during phosphodiester bond formation makes this polymerization reaction irreversible
67
Describe transcription termination process in prokaryotes (not the certain sequences)
When the end of a gene is reached, the process of RNA transcription must be terminated.
**termination sequenves** in the DNA lie near the end of a coding sequence of a gene.
These sequences release the RNA transcript and release the transcription complex.
68
Describe the two terminator sequences in a prokaryotic DNA template strand
Rho independent terminator sequences
1. These are going to contain the inverted repeated sequenecs followed by a sdtring of 6 adenine nucleotides
2. The inverted repeat sequence is going to be transcribed into the RNA sequence
3. This will cause the folding of the RNA transcript into a hairpin loop which causing transcription to pause
4. RNA transcript separates from the template, and terminates transcription
Rho-dependent termiantor sequences
-Uses a specific prokaryotic protein/Rho factor which can bind to and use ATP energy to move along the formed RNA transcript while unwinding it from the DNA tempalte.
-this terminator sequences destabilize the interactions between RNA and DNA template, leading to the release of the transcript and transcription complex.
69
How does translation occur in a prokaryote?
Tranlsation is paired with transcription in a prokaryote
Sometimes the process of translating mRNA into a polypeptide can begin even before transcription is completel
The ribsome complex is latched onto mRNA as it is being transcribed
This happens in the same space and corodinated because prokaryotes are not compartmentalized and have no nuclear envelope/membrane that is able to seperate transcription and translation
Prokaryotic genes are organized differently as well
This will lead to characterisitic differences between mRNA transcripts that are produced by prokaryotes vs eukaryotes.W
70
Why does translation occur the way it does in prokaryotes?
Because the genetic information/nuclei of a porkaryote lackcs compartentalization so the processes occur simulatensouly
71
Difference between eukaryotic and prokaryotic mRNA processing
-in eukaryotes, only sigma factor proteins are required and in prokaryotes many general transcription factors are required for the binding of the RNA polmyerase to the promoter site
-promoter regions in DNA of eukaryotes are much more complex
-eukaryotes have 3 different RNA polymerase
72
The three different RNA polymerase and their functions in eukaryotic cells
RNA polymerase 1
-transcribes the genes for ribosomal RNA
RNA polymerase 3
-transcribes genes for the transfer of RNA (tRNA)
-transcribes untranslated RNAs
1 and 3 both transcribe structural, non-coding RNAs
RNA polymerase 2
-transcribes the messenger RNAs
73
Intiation for eukaryotic transcription
There are promoter consensus sequences which are required in order to set up a transcription initiation complex for the particular RNA polymerase and gene beign transcribed
74
How do transcription and translation occur in eukaryotes?
They are physically seperated in the cell by a nuclear membrane.
75
What are post transcriptional modifications, what is the purpose of them?
After transcription is complete and the termination sequence is reached so that the polypeptide is able to be released, the protein will undergo a post transcriptional modification.
-addition of a 5' cap and 3' poly A tail
-ensure stability of mRNA molecule
-export from nucleus is protected against enzymes that target bonds
-helps with attachment of ribosomes and intiation of translation once mRNA reaches cytoplasm
76
Explain the 5' cap + the entire process
This is a post transcriptional modifcation and it ensures that the mRNA is
A 7-methylguanonsine (modified guanonsine) is attached to the terminal 5' end phosphate from mRNA molecule through a **triphosphate linkage** by a **phodphtase enzyme** and **guanosyl tranferase** which both catalyze the attachment of the 7-methylguanosine as the 5' cap.
77
Explain the poly (A) tail -> these are added to the 3' end of a transcribed mRNA molecule for post transcriptional modifciation
A **polyadenylation signal sequence (AATAAA)** is transribed from the DNA template near the end of the gene sequence.
Once transcribed, the mRNA is cleaved, and a poly(A) polymerase enzyme is able to add 150-200 adenine nucleotide bases to the 3' end of the RNA-transcript process
This is referred to as **polyadenylation** which is coordinated with termiantion of transcription
78
Splicing
Splicing is a way of removing large parts of non-coding DNA sections called introns
Introns are not coded into a message and does not make a protein
-these are important for gene expression but will not code for an amino acid
-RNA polymerase makes both introns and exons
Eukaryotic DNA sequence is split into many segments of exons and introns.
Process:
Occurs at the end of each intron
**spliceosomes** are molecular machines made from SnRNPs (small nuclear ribonucleoproteins) which are able to catalyze the RNA splicing which are able to recognize the splice site within the intron
At the start of RNA splicing, a splicesosome attaches onto the desginated splice site and form a complementary base pairing
The splicesosome complex then catalyzes a reaction so that OH group on the branch site effectively "attacks" to form a new phosphodiester bond with a nucleotide at a donor site
This forms a *lariat intermediate loop*
The 3' hydroxyl group at the cut end of the 5' **EXON** at the donor site is able to "attack" the phosphidiester beond at the 3' acceptor site
This cuts the 5' end of the exton and then releases the lariat intermediate loop.
The lariat quickly breaks down into individual nucleotides
Spliced exons are adjacent in the processed RNA
79
How is transription terminated in eukaryotes
Termination sequence is different depending on the type of RNA polymerase that is being used for transcription
I = transcription is terminated by using a specific eukaryotic termination factor in a similar manner as a prokaryotic rho-dependent termination
II = depends on poly(A) dependent mechnaims of termination
-termination coupled with addition of a poly A adenine tail (polyadenylation)
III = similar to rho-independent termination in prokaryotes
80
What happens after transcription is completed in the nucleus?
The mRNA is exported from the nuclear compartment of cytoplasm through nuclear membrane pore complexes in the nuclear membrane
-nuclear pores trasnport proteins, carbohydrates, and other signalling molecules into the nucleus
81
Who found out the number of nucleotides that are needed for coding one amino acid?
George Gamow
-he formed an RNA Tie club with 4 nucleotide members and 20 for each amino acid.
-He thought 1 would only produce 4 amino acids so it would not be sufficient enough
2 would only produce 16 amino acids
3 would produce 4x4x4 = 64 amino acids
- there would be some redundancy but it would accomodate all 20 amino acids
82
What did Marshall Nireberg and Johann Matthaei discover
They discovered the first letter of code in 1961.
They put all the components needed for protein synthesis in a tube (RNA template, nucleotides, ribosomes, amino acids, and ATP)
- they made a string of uracil nucleic acids and then this produced a repeated simple polypeptide sequence with identical Phenylalaline
-and when they put alternating uracil and cysosines the strand was always serine and leucine amino acids
This all suggested that three nucleotides make up a **codon** which will code for a specific amino acid
83
What direction are codons read in?
5'-> 3' direction
84
What is the coding strand
Also known as the non-template strand it is the strand that has the same nucleotide sequence/codons as the mRNA just differing in the U and T nucleotides
85
Codon vs anticodon
Codon = the 3 nucleotide sequence which codes for an amino acid
Anti-codon= the 3 nucleotide sequence which pairs with the DNA strand (just the opposite pairing)
86
What is the start codon
AUG (Methionine)
87
What are the stop codons
UAA, UAG, UGA
These do not code for an amino acid, they are found at the end of a protein coding sequence (made in transcription and enacted in translation)
Signal that translation is complete
88
?/64 code for amino acids?
61
89
What does it mean by genetic code being umabiuguous?
This means that genetic code is redundant and a unique triplet codon will always code for a specific amino acid and never more than one
This is very important as the cell has to produce the correct proteins with the appropriate, structure, sequence, and functionality
The unambiguous nature ensures there will never be confusion within amino acid placement in a growing polypeptide chain
One amino acid can be multiple codons but one codon codes for only one amino acid
90
What is the non-coding strand? Vs the coding?
The non-coding strand is the template DNA because it simply serves as a template for RNA transcription and does not actually code for anything
Coding strand would be the non-template strand since it has the same nucleotide sequence/codons of the transcribed mRNA
91
What is the reading frame
The entire continuous sequence of a gene that begins at a triplet AUG start codon (Met) and ends at a triplet stop codon read in the 5' to 3' direction
92
WHAT DIRECTION IS MRNA READ
5' TO 3' DIRECTION
REMEEMBERRRRRR
93
First, second, third reading frame meaning
First starts from the first nulceotide from the 5' end and the second is from the second nucleotide from 5' end and third is the third nucleotide form 5' end.
94
What happens if nothing is known about the genes on a particular DNA molecule (for reading frame)?
Each strand of the double stranded DNA could be the template strand and you have 6 reading frames 3 on one and 3 on the other
95
What did Francis Crick, Leslie Barnett, Sydney Brenner, and Richard Watts-Tobin discover?
That code was written out in triplets
-this was because if one-two nucleotide was removed or added it would change the entire reading frame
96
What is a frameshift mutation
A mutation that occurs due to the removal or addition of 1-2 nucleotides into an amino acid sequence
-include insertion and deletion mutations
97
What are the intermediates between mRNA and polypeptides
tRNA
They are the translator between the two codes
98
What is the "primary transcript"
The transcript of mRNA before any post modifications occur
5' end cap
3' poly A tail
Intron splicing
99
anti sense strand =
Minus strand =
PLus strand =
anti sense strand = noncoding
Minus strand = noncoding
PLus strand =coding strand
100
Why is it assumed that genetic code must have been established early in the history of life?
Because the genetic code is shared almost universally by organisms. It is the blueprint of life.
-the same codons (sequences of three nucleotides) typically are the same across many diverse species
-the genetic transmission of infromation from one generation to the next
-the complexity of the genetic code which remains relatively unchanged 64 codons for 20 amino acids 3 stop codons and 1 start codon.
101
What are expcetions to the universal genetic code?
Paramecium: UAA and UAG are not stop codons -> they code for GLUTAMINE
Plastids
Mitcodhinra
These both have their own DNA which code for certain proteins
Yeast - CUA codes for Threnonine
Mammalian mitochondria - CUA codes for leucine
102
Paramecium excception code
UAG and UAA stop codons code for Glutamine
103
Yeast excception code
CUA codes for Threonine
104
Mammalian excception code
CUA codes for Leucine
105
What is retinoblastoma
This is a genetic mutation of the Retinoblastoma protein which has the ability to block cell cycel progression (acts like a cell cycle break) (overgrowth and tumor growth) by inhibting the E2F transcription factors when unphosphorylated
This causes a tumour on the retina which can quickly spread to other areas of the body
106
What can be used to predict the areas where tumours will develop?
Karaotype analysis
107
How is retinoblastoma treated?
They are treated via chemotherapy drugs which contain liposomes that contain chemotherpay drugs enclosed int them.
Chemotherapy drugs are targeted to certain areas and kill cancer cells
108
Other health conditions related to transcription errors:
Diabetes 1 and 2
Alzheimer's disease
Parkinson's disease
Aging and Cancer
109
